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UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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Next release: 2018-11-12 #113

Closed HenrikBengtsson closed 5 years ago

HenrikBengtsson commented 5 years ago

FYI, I ran the tests overnight and took the freeddom to release LG3_Pipeline 2018-11-12 (just now), which is now also the new default for module load CBC lg3 on TIPCC.

ivan108 commented 5 years ago

Great, thanks! I see we still have ~30 open issues, what are current or next priorities?

HenrikBengtsson commented 5 years ago

I added you as a collaborator a while ago. As a collaborator, you should be able to set labels and milestones on issues. Feel free to go through issues and update the milestone to 'Next Release' for things you think we should work on next. That'll give us a good first iteration on what to work on/discuss to work on.

In the bigger picture, I think we still need to consolidate the software stack (so we can configure it in a single location). The same goes for the annotation data/reference files. When we have that in place, we will be able to start migrating to non-legacy version ofl say, Java, R, Python.

HenrikBengtsson commented 5 years ago

Importantly, I also think it's time for you to start committing as yourself and not via Joe's GitHub credentials. Please do that. When you've got that up and running, I'll also rewrite the Git commit history so those old commits of yours are associated with you - the latter is a big change so it'll require some coordination between the two of us.

ivan108 commented 5 years ago

From my perspective, since basic pipeline is working fine, the highest priority is to add the other two "modules" we talked about: exomeQualityPlots and copy number (PSCN). As you know both are maintained by Stephanie on github. I guess we can treat those "modules" as any other external software: install it in some directory and create a variable pointing to it's location. We still need to create launching interface integrated into LG3 pipeline. What do you think?

Thanks as always!

HenrikBengtsson commented 5 years ago

Would a first step be to get those two steps/pipeline in by creating symbolic links under LG3_HOME, e.g. $LG_HOME/exomeQualityPlots and $LG_HOME/pscn and then provide run scripts for those as well? An alternative to run scripts is to get the lg3 run <step> (Issue #84) going first such that there will be one or more lg3 run pscn step(s).

I think it's helpful to keep the LG3_Pipeline and those other reposes separated for now, especially until LG3_Pipeline has settled. The current amount of commit traffic will clutter up those other projects too much.

ivan108 commented 5 years ago

I just added 3 launching scripts for exomeQualityPlots pipeline: runs_demo/_runQC?

HenrikBengtsson commented 5 years ago

Closing this one since the purpose of this issue was related to the 2018-11-12 release.

If there are outstanding tasks/issues in the comment, please create new, separate issues for those.